Namd¶

Installed versions¶

Resource	Version
Dardel-GPU/cpe23.12.gpu	3.0b-rocm
Dardel/cpe23.12	3.0b

General information¶

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. For more information see the NAMD homepage.

NAMD is available to users as a module - we have a non-exclusive, non-commercial use license for academic purposes.

Citations

See the Acknowledge the TCB Group p

age for specifics on how to acknowledge the use of NAMD.

How to use¶

Example job script for a regular NAMD run on 2 nodes:

#!/bin/bash
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=128
# load the NAMD module
ml PDC/<version>
ml NAMD/3.0b
# Run namd
srun namd2 input.namd > output_file

Example job script for a 2-node shared-memory NAMD run with one MPI process per node:

#!/bin/bash
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=1
# load the NAMD module
ml PDC/<version>
ml NAMD/3.0b
# Run namd
srun -n 2 namd2 +ppn 31 input.namd > output_file

Example job script for a 2-node shared-memory NAMD run with 4 MPI processes per node and explicit mapping of communication and processing cores:

#!/bin/bash
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=4
# load the NAMD module
ml PDC/<version>
ml NAMD/2.14
# Run namd
srun -n 8 namd2 +ppn 7 +pemap 1-7,9-15,17-23,25-31 +commap 0,8,16,24 input.namd > output_file